\docType{class}
\name{annotationByGenicParts-class}
\alias{annotationByGenicParts}
\alias{annotationByGenicParts-class}
\title{An S4 class for overlap of target features with gene annotation}
\description{
  This object is desgined to hold basic statistics and
  information about genomic feature overlaps. It extends
  \code{\link[methylKit]{annotationByFeature}} class. The
  class contains an additional slot for data containing
  distance to nearest transcription start site (TSS).
}
\section{Slots}{
  \describe{ \item{\code{members}}{a matrix showing overlap
  of target features with gene annotation features}
  \item{\code{annotation}}{a named vector of percentages of
  overlap between feature and gene annotation}
  \item{\code{precedence}}{a named vector of percentages of
  overlap between feature and gene annotation}
  \item{\code{num.annotation}}{a named vector of numbers of
  overlap between feature and gene annotation}
  \item{\code{num.precedence}}{a named vector of numbers of
  overlap between feature and gene annotation}
  \item{\code{no.of.OlapFeat}}{a named vector of numbers of
  overlap between gene annotation and the feature}
  \item{\code{perc.of.OlapFeat}}{a named vector of
  percentages of overlap between gene annotation and the
  feature } \item{\code{dist.to.TSS}}{a data frame showing
  distances to TSS and gene/TSS names and strand} }
}
\examples{
data(methylKit)
gene.obj=read.transcript.features(system.file("extdata", "refseq.hg18.bed.txt", package = "methylKit"))

# the following function returns an annotationByGenicParts object
ann=annotate.WithGenicParts(methylDiff.obj, gene.obj)
}
\seealso{
  see \code{\link[methylKit]{annotate.WithGenicParts}} on
  how to create this object, see following functions that
  operates on this object
  \code{\link[methylKit]{getTargetAnnotationStats}},
  \code{\link[methylKit]{getMembers}},
  \code{\link[methylKit]{getAssociationWithTSS}},
  \code{\link[methylKit]{getTargetAnnotationStats}},
  code{\link[methylKit]{getFeatsWithTargetsStats}},\code{\link[methylKit]{plotTargetAnnotation}}
}

